Download - Outline of Enzyme Introduction Enzyme kinetics - Mechanistic models for simple enzyme kinetics - Effect of pH and Temperature Immobilized Enzyme System

Outline of EnzymeIntroduction

Enzyme kinetics- Mechanistic models for simple enzyme kinetics- Effect of pH and Temperature

Immobilized Enzyme System- Method of immobilization- Diffusional limitations - Electrostatic and steric effects

Large-scale production and application of enzyme.

What is Enzyme?An enzyme is a protein molecule that is a biological

catalyst with the following characteristics.

• Effective to increase the rate of a reaction. Most cellular reactions occur about a million times faster than they would in the absence of an enzyme.

• Specifically act with one reactant (called a substrate) to produce products. maltase that converts maltose to glucose

• Be regulated from a state of low activity to high activity and vice versa. e.g. some enzyme activity is inhibited by the product.

• Be versatile: More than 3000 enzymes are identified

EnzymeEnzyme has high molecule weight (15,000< mw<

several million Daltons).

Holoenzyme is an enzyme contains non-protein group.

Such non-protein group is called cofactor such as metal ions, Mg, Zn, Mn, Fe

Or coenzyme, such as a complex organic molecule, NAD, or vitamins.

Apoenzyme is the protein part of holoenzyme.

Holoenzyme = apoenzyme + cofactor (coenzyme)

Enzyme nomenclatureEnzyme is named by adding the suffix –ase

- to the end of the substrate that is to be converted to the desired product.

e.g. urease that changes urea into ammonium carbonate.protease that converts protein or polypeptides to

smaller molecules such as amino acids.

- to the reaction catalyzed.

e.g. phosphoglucose isomerase that converts glucose-6-phosphate to fructose-6-phosphate.

Alcohol dehydrogenase that catalyzes the removal of hydrogen from alcohol.

Enzyme classification

International Classification of Enzymes by the International Classification Commission in

1864.

Enzymes are substrate specific and are classified according to the reaction they catalyze.

Enzyme Nomenclature, 1992, Academic Press, San Diego, California, ISBN 0-12-227164-5.

http://www.chem.qmul.ac.uk/iubmb/enzyme/

Enzymes can be classified into six main classes:

- Oxidoreductases: catalyze the oxidation and reduction e.g. CH3CH2OH → CH3CHO+H+

- Transferases: catalyze the transfer of a functional group (e.g. a methyl or phosphate group) from one molecule (called the donor) to another (called the acceptor).

A–X + B → A + B–X

- Hydrolases:catalyze the hydrolysis of a chemical bond. A–B + H2O → A–OH + B–H, e.g. peptide bond


- Lyases:catalyze the breaking of various chemical bonds by means other than hydrolysis and oxidation, often forming a new double bond or a new ring structuree.g. CH3COCO-OH → CH3COCHO (dehydratase)

- Isomerases:catalyse the interconversion of isomers. e.g.phosphoglucose isomerase that converts glucose-6-phosphate to fructose-6-phosphate.

- Ligases:catalyse the joining of two molecules by forming a new chemical bond, with accompanying hydrolysis of ATP or other similar moleculesATP + L-tyrosine + tRNATyr = AMP + diphosphate +

L-tyrosyl-tRNATyr



Each main class contains subclasses, subsubclasses and subsubsubclasses. There are four levels of classes in total.

e.g. Reaction: CH2CH2OH+NAD+→CH3CHO (acetaldehye)+NADH+H+

Systematic name: alcohol NAD oxidoreductase (1.1.1.1)

Trivial name: alcohol dehydrogenase

1. Oxidation-reduction reaction

1.1 Acting on R-OH group of substrates

1.1.1 Requires NAD+ or NADP+ as hydrogen acceptor

1.1.1.1 Specific substrate is ethyl alcohol

Mechanism of enzyme catalysis

What is a catalyst?

• A catalyst is a substance that accelerates the rate (speed) of a chemical reaction without itself being consumed or transformed.

• It participates in reactions but is neither a chemical reactant nor chemical product.

S + C (catalyst) P + C (catalyst)

S P


• Catalysts provide an alternative pathway of lower activation energy for a reaction to proceed whilst remaining chemically unchanged themselves.

Free energy change

• Catalysts lower the activation energy of the reaction catalyzed by binding the substrate and forming an catalyst-substrate complex which produces the desired product.

• Catalysts lower the activation energy of the catalyzed reaction, but does not affect free energy change or equilibrium constant.


The reaction rate v is strongly affected by the activation energy of the reaction.

v = k*f(S)-f(S) denotes the function of substrate concentration

-k is the rate constant which can be expressed by

Arrhenius equation (H.S. Fogler, Chemical Reaction Engineerng,

Prentice-Hall Inc., 2005)

k=A*exp(-Ea/R*T)

A is a constant for a specific system,

Ea is the activation energy,

R is the universal gas constant, and T is the temperature (in degrees Kelvin).

When Ea is lowered, k is increased, and so is the rate.


• Catalysts do not affect free energy change or equilibrium constant of the catalyzed reaction.

Free energy (G) is the energy stored in the bonds of a chemical that can be harnesses to do work.

Free energy change (ΔG) of a reaction refers to the change between the free energy in the product (s) and that in the substrate(s).



• For uncatalyzed reaction,

free energy change ΔG, uncatalyzed=G(P)-G(S)

• For catalyzed reaction,

free energy change ΔG, catalyzed=G(P)-G(S)

Therefore, ΔG, uncatalyzed= ΔG, catalyzed


S P

For an example,


• Free energy change determines the reaction equilibrium – the maximum amounts of the product could be theoretically produced.

• Reaction equilibrium is represented by reaction equilibrium constant Keq,=γp[P]/ γs[S]

- ΔG, uncatalyzed=RTln Keq

[ ] represents the concentration of the compounds.

γp and γs are activity constants of the product and the substrate, respectively.


S P


• Catalysts can not increase the amounts of the product at reaction equilibrium.

• Catalysts can only accelerate the reaction rate to reach the reaction equilibrium.


• Enzymes are catalysts and have the characteristics of common catalysts.

Particularly,

• Enzymes are

- Efficient

- Specific

- regulated

- versatile

Efficiency of Enzyme CatalysisFor an example, in the reaction of

decomposition of hydrogen peroxide, the activation energy Ea,o of the uncatalyzed reaction at 20oC is 18 kcal/mol, whereas that for chemically catalyzed (Pt) and enzymatically catalyzed (catalase) decomposition are 13 kcal/mol (Ea,c) and 7 kcal/mol (Ea, en), respectively.

Compare the reaction rates at these three different conditions.

The forward reaction rate r (moles/L-s),

r = k*f(H2O2)

k is the forward reaction rate constant, f(H2O2) is a function of substrate perioxide concentration.

Efficiency of Enzyme Catalysis

2H2O2 2H2O + O2

If k is represented by k0, kc, and ken , respectively, for the uncatalyzed, chemically catalyzed (Pt) and enzymatically catalyzed reactions, the corresponding reaction rates (r0, rc, ren) can be expressed as follows

r0 = k0*f(H2O2)

rc = kc*f(H2O2)

ren = ken*f(H2O2)

The ratio of the chemically catalyzed rate to the uncatalyzed rate can be calculated by as follows:

rc /r0 = kc*f(H2O2)/k0*f(H2O2)

Similarly, The ratio of the enzymatically catalyzed rate to the uncatalyzed rate can be calculated by as follows:

ren /r0 = ken*f(H2O2)/k0*f(H2O2)

At 20oC, with the same initial concentration of reactant hydrogen peroxide, f(H2O2) remains the same for the above three process at initial conditions, the initial reaction rates vary with the rate constants.

rc /r0 = kc/k0

ren /r0 = ken/k0

Using Arrhenius Equations yields,

rc /r0 = kc/k0 = (A*exp(-Ea,c/R*T))/(A*exp(-Ea,o/R*T))

ren /r0 = ken/k0 = (A*exp(-Ea,en/R*T))/(A*exp(-Ea,o/R*T))

Where Ea,o, Ea,c and Ea,en are activation energy for uncatalyzed reaction, chemically catalyzed and enzymatically catalyzed reactions, respectively.

A is a constant and remains same for the specific system, the rate ratios could be simplified to:

rc /r0 = (exp(-Ea,c/R*T))/(exp(-Ea,o/R*T))

ren /r0 = (exp(-Ea,en/R*T))/(exp(-Ea,o/R*T))

When T= 20oC = 273+20 (K) = 293 K,

Ea,o = 18 kcal/mol, Ea,c = 13 kcal/mol (Ea,c) and

Ea, en =7 kcal/mol, respectively.

R = 8.314 J mol-1K-1 , 1 cal = 4.18 J.

Then substituting the parameters in the rate ratio eqns. with these values, yields,


= (exp(-13000*4.18/8.314*293))/(exp(-18000*4.18/8.314*293))

=?


=(exp(-7000*4.18/8.314*293))/(exp(-18000*4.18/8.314*293)

=?

When T= 20oC = 273+20 (K) = 293 K,

Ea,o = 18 kcal/mol, Ea,c = 13 kcal/mol (Ea,c) and

Ea, en =7 kcal/mol, respectively.

R = 8.314 J mol-1K-1 , 1 cal = 4.18 J.

Then substituting the parameters in the rate ratio eqns. with these values, yields,


= (exp(-13000*4.18/8.314*293))/(exp(-18000*4.18/8.314*293))

=5.1X103


=(exp(-7000*4.18/8.314*293))/(exp(-18000*4.18/8.314*293)

=1.4X108

Enzyme catalysis is efficient!

- If it takes 1 hr to complete the reaction with enzyme

- it needs to take

1.4X108 hrs = 5833333 days = 15981years

to complete the same reaction without enzyme catalysis.

Specificity of Enzyme Catalysis

• Much of the catalytic power of enzymes comes from their bringing substrates together in favorable orientations to promote the formation of the transition states in enzyme-substrate (ES) complexes.

• The substrates are bound to a specific region of the enzyme called the active site.

• Most enzymes are highly selective in the substrates that they bind. The catalytic specificity of enzymes depends in part on the specificity of binding.

E + S ES E + P

Specificity of Enzyme Catalysis

Lock-and-Key Model of Enzyme-Substrate Binding (Emil Fischer ,1890)

.

In this model, the active site of the unbound enzyme is complementary in shape to the substrate

The Active Sites of Enzymes Have Some Common Features

The active site of an enzyme is the region that binds the substrates (and the cofactor, if any).

• It also contains the residues that directly

participate in the making and breaking of bonds. These residues are called the catalytic groups.

• The interaction of the enzyme and substrate at the active site promotes the formation of the transition state.


• The active site is a three-dimensional cleft formed by groups that come from different parts of the amino acid sequence.

• The active site takes up a relatively small part of the total volume of an enzyme. The "extra" amino acids serve as a scaffold to create the three-dimensional active site from amino acids that are far apart in the primary structure.

• Substrates are bound to enzymes by multiple weak attractionsInteractions in ES complexes are much weaker than

covalent bonds.


• The specificity of binding depends on the precisely defined arrangement of atoms in an active site.

- The lock-and –key model (Emil Fischer): The enzyme has a fit shape before the

substrate is bound.

- The Induced-Fit Model (Daniel Koshland, Jr. 1958)Enzymes are flexible and the shapes of the

active sites can be markedly modified by the binding of substrate.

Induced-Fit Model of Enzyme-Substrate Binding. In this model, the enzyme changes shape on substrate binding.

The active site forms a shape complementary to the substrate only after the substrate has been bound.

Summary of Introduction

• Enzyme classification

• Enzyme have common catalytical features- decrease the reaction activation energy- does not affect equilibrium

• Enzyme special catalytic features- Efficient- Specific- regulated - versatile

Enzyme kineticsMichaelis-Menten kinetics or saturation kinetics

which was first developed by V.C.R. Henri in 1902 and by L. Michaelis and M.L. Menten in 1913.

This model is based on data from batch reactors with constant liquid volume.

- Initial substrate, [S0] and enzyme [E0] concentrations are known.

- An enzyme solution has a fixed number of active sites to which substrate can bind.

- At high substrate concentrations, all these sites may be occupied by substrates or the enzyme is saturated.

Saturation Enzyme Kinetics

Enzyme kinetics

E.g. a simple reaction scheme that involves a reversible step for enzyme-substrate complex formation and a dissociation step of the ES complex.

][][

2ESk

dt

Pdv

K1

EPk

ES 2E+SK-1

where the rate of product formation v (moles/l-s, g/l-min) is

Ki is the respective reaction rate constant.

Enzyme kinetics

The rate of variation of ES complex is

Since the enzyme is not consumed, the conservation equation on the enzyme yields

][2][1]][[1][

ESkESkSEkdt

ESd

][]0[][ ESEE

Download - Outline of Enzyme Introduction Enzyme kinetics - Mechanistic models for simple enzyme kinetics - Effect of pH and Temperature Immobilized Enzyme System

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